Unable to end the program, they leave the holodeck running and exit the holodeck via site-to-site transport. After being trapped on the subspace sandbar for several days, weapons fire is detected on the holodeck. Paris and Tuvok investigate and discover that photonic lifeforms have mistaken the holodeck program for reality and are now at war with Doctor Chaotica. Apparently, these lifeforms are explorers and believe that they are making theirfirst contact with Humans. Unfortunately, Chaotica believed they were aliens of the fifth dimension and killed one of the lifeforms' emissaries. Tuvok and Paris try to explain to the lifeforms that they are in a simulation but the aliens refuse to believe, as their "sensors" can't pick up "biochemical lifeforms", which they think are artificial.

Paris and Tuvok brief the senior staff on what they've found. They decide the only way out is to play along as the characters in Captain Proton. Paris and Kim resume their previous roles. CaptainJaneway is enlisted to play Queen Arachnia. Her assignment is to get Doctor Chaotica to lower his lightning shield. With some help from B'Elanna Torres, The Doctor will pose as the President of Earth. In the program, he encounters one of the photonic aliens and convinces them that Captain Proton is an agent of Earth and is not a threat to them, but Doctor Chaotica is. He is able to convince the photonic aliens to leave once Captain Proton defeats Doctor Chaotica.

Janeway, as Queen Arachnia, eventually completes her mission only after agreeing to become Chaotica's bride and unleashing the pheromone on his right hand. Unfortunately, she tries to have him deactivate the shield by force but he imprisons her. But she is able to use the pheromone on his henchmen and disable the men and the Lightning shield. Afterward, Paris, as Captain Proton, destroys Chaotica's death ray. Chaotica is then fatally wounded with the destruction of the death ray. As the others arrive, Chaotica declares that this isn't the last they will see of him.

Once the photonic aliens have left, Voyager is able to continue on its way.

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"Coffee, black."
"Um, sorry captain. We lost two more replicators this morning..."
"Listen to me very carefully because I'm only going to say this once. Coffee, black."
"...Yes ma'am."

- Janeway and Neelix

"Well, he's been attacking the aliens with his death ray."
"It's a shame we don't have one."

- Paris and Tuvok

"This is how you've been spending your free time?"
"Well, I've, uh, been studying how past generations view the future."
"And...?"
"Well (chuckles), it didn't work out quite as black-and-white as they imagined."

- Janeway and Paris, with an apparent pun on the monochromatic environment of Captain Proton.

"One more thing. If you have trouble with Chaotica, or you can't get to the death ray, you can always uncork the pheromones."
"I beg your pardon?"

- Paris and Janeway

"Ah, I see you've kept my pheromones. I didn't realize you were the scent-imental type."

- Janeway as Queen Arachnia

"Let me get this straight: trans-dimensional aliens have mistaken your Captain Proton simulation for reality."
"Yes ma'am."
"And now an armed conflict has broken out between these aliens, and Chaotica's holographic army."
"Yes ma'am. His army of evil."

-Janeway and Paris

"The Destructo beam on my rocket ship can disable the death ray, but only if someone gets inside the Fortress of Doom and can shut down the lightning shield."

- Janeway, as Queen Arachnia after harmlessly absorbing a holographic blast from one of Chaotica's goons

" I don't know how to tell you this..."(shoots Chaotica with ray gun)"but the wedding's off!"

- Janeway as Queen Arachnia, to Dr. Chaotica

"Looks like he burned out a resistor.'"
"A what?"

- Paris and Tuvok, as Paris repairs Satan's Robot

"Intercepted communications between Dr Chaotica and Arachnia. Stop. Chaotica at war with aliens from fifth dimension. Stop. Must strike now to disable death ray.'"
"Stop. Please summarize the message."

This episode's plot was conceived as a way to keep as much action as possible off the bridge, due to a fire which damaged that set (for more information, see VOY Season 5). [X]wbm

The success of The Adventures of Captain Proton holodeck program, having been introduced earlier in the fifth season, was a prominent inspiration on the creation of this episode. (Cinefantastique, Vol. 31, No. 11, pp. 44 & 48) The installment, in common with the holoprogram featured in it, was also meant as a parody of Flash Gordon. (Cinefantastique, Vol. 31, No. 11, p. 45; Cinefantastique, Vol. 30, No. 9/10, p. 103) Rick Berman recalled of the episode, "We decided to go high-camp [...] [and] black-and-white with it." (VOY Season 5 DVD, "Braving the Unknown: Season Five") Episode co-writer Bryan Fuller found the writing of the episode to be very enjoyable, later remarking, "'Bride of Chaotica!', which I wrote with Mike Taylor was just a blast to write [....] We watched hours of old Flash Gordon serials and just got into the genre and had some fun." (Star Trek Magazine issue 114, p. 36) The episode's development was also a thrill for supervising producer Kenneth Biller, who was involved in the episode's rewrite process in an uncredited capacity. He reminisced, "It was fun to write that inflated language, and come up with funny gags, and funny dialogue. It was fun to do a kind of comic romp." (Cinefantastique, Vol. 31, No. 11, p. 45)

Having been very eager to work on the Captain Proton set, Tuvok actor Tim Russ was thrilled when the time came for him to do so. "It was very nice to be able to go in for a minute, under the auspices of investigating what was going on that wasn't quite right about it, and be able to work on the set, and be able to see it back in black and white. I thought it was very cool," Russ enthused. "I really enjoyed having an opportunity to do that." (Cinefantastique, Vol. 31, No. 11, p. 39)

Tim Russ also appreciated that this episode allowed him to perform some comedy. He laughed, "Between the robot and Paris, there is a lot to play off of there, quite a bit actually [....] Paris is so careless and so off-center. It works very well against Tuvok's straight and linear way of doing things. 'Chaotica' was a prime example, and the writers gave me several zingers to throw him." (Cinefantastique, Vol. 31, No. 11, p. 39)

Kate Mulgrew was delighted to perform Janeway's turn as Queen Arachnia, commenting, "That was the greatest fun. That was just wild fun. That was cut loose fun time. I mean those opportunities are few and far between for the captain. And I think everybody said, 'Oh well, let's just let Kate have a ball.' And I did." (Star Trek: Voyager Companion, p. 283) Mulgrew also remarked, "I was the bride of Chaotica. Only the funniest man I have ever met in my life. When he electrocuted himself, I wet my pants. It was just outrageous. And I go to seduce him. It's a cartoon! [....] I was playing a '40s movie star. It was outrageous, it was so much fun and I hope the viewers liked it as much as I liked doing it. [I] loved the double punch, [I] loved the curve and when there was a little levity attached to it... Heaven!" (VOY Season 5 DVD, "Braving the Unknown: Season Five")

Mitch Suskin, who supervised the visual effects of this outing, remembered that the lead-up to the making of the episode was an exciting time, saying, "I think everybody knew it was going to be really fun to work on, so that it emulates that 1940s serial look without being completely over the top." (Cinefantastique, Vol. 31, No. 11, p. 48)

Set decorator James Mees found that the episode's production was highly enjoyable, later reminiscing, "We had a great time on Captain Proton and 'Bride of Chaotica!' [....] To rethink things so that they would photograph properly in black and white was amazing." (Star Trek: The Magazine Volume 3, Issue 3, p. 85)

The Fortress of Doom's interior was designed to look highly expansive. Production Designer Richard James remarked, "When we did the palace, that gave us a chance to even do a bigger scale and everything. And of course, we went for as big a scale as we could achieve. I think we went pretty high with some of the columns and so forth." (VOY Season 5 DVD, "Braving the Unknown: Season Five")

The bridge scenes in this episode were actually shot weeks after the rest of the episode. [X]wbm

Mitch Suskin noted that Captain Proton's rocket ship, which was designed by visual effects producer Dan Curry, looks much like the Flash Gordon ship and that the visual effects artists chose to represent the Fortress of Doom's exterior by intentionally making repeated reuses of a certain angle of the fortress, whose outside was actually a digital matte painting done by Eric Chauvin. (Cinefantastique, Vol. 31, No. 11, pp. 48-49)

Rick Berman had words of high praise for this outing. "I thought it was a ball," he enthused. (VOY Season 5 DVD, "Braving the Unknown: Season Five")

Ken Biller, however, had a problem with the installment. "I thought that, while Kate [Mulgrew]'s performance in the episode was, at certain points, a wonderful comic performance, I think that there was a mistake either in the performance choices or in the direction of it," Biller criticized. "Captain Janeway playing Queen Arachnia made sense, up to a certain point. There was a point at which, clearly, she had gotten what she needed to get. For some odd and, I thought, unexplained reason, she continued to assume this role, as opposed to being Captain Janeway wearing the costume, finishing up the mission. I just thought it got over-the-top." (Cinefantastique, Vol. 31, No. 11, p. 45)

Contrastingly, James Mees was very enthusiastic about the episode. In a 2002 interview, he remarked, "We were really disappointed that that show didn't get nominated for an Emmy, because the art direction was spectacular [....] And then, of course, it was so over the top; I still watch that and laugh." (Star Trek: The Magazine Volume 3, Issue 3, p. 85)